SG 4.0.33 & PS 2.0.25

[CarlosHorro]

Metamorpheus available
Other bugfixes

[bernt-matthias]

Hey @CarlosHorro please add this here: #584

I also would prefer to have a version fixing compomics/peptide-shaker#445 as well. To me it seems that PS does not work at all due to this (or am I wrong?) and then there is not much use in updating SG since both tools are coupled, or?

[bernt-matthias]

A test using MM would also be cool.

[CarlosHorro]

Hey @CarlosHorro please add this here: #584

Yes, thank you, I forgot about it...

I also would prefer to have a version fixing compomics/peptide-shaker#445 as well. To me it seems that PS does not work at all due to this (or am I wrong?) and then there is not much use in updating SG since both tools are coupled, or?

Well, I might be forgetting something but as far as I know saying that "PS does not work at all" sounds a bit excessive?
SG and PS are not strictly coupled, it depends on the releases done to them both. They may work whist there are no big version differences between them.
I would like to work on that issue, but it is a separated one that will require quite an effort and I am not sure when I will be able to do it, so it is better to go step by step and fix this issue now (MM release) and that other issue in a specific release for it.

A test using MM would also be cool.

I might add it, but that would require to add mzml files to the repo as input to MM and they are usually too big to be included there...

Greetings,
Carlos

[CarlosHorro]

Well, now I see what you meant when you said that PS did not work at all. But paths.txt related stuff has not been touched for a long time and PS worked, so PS current failed tests should be related to another issue... I will try to dig into this as soon as possible, although now there are many holidays coming here in Norway :-)

Greetings,
Carlos

[bernt-matthias]

Well, now I see what you meant when you said that PS did not work at all

If this is a non critical error we could grep -v java.io.FileNotFoundException: /usr/local/share/peptide-shaker-2.0.25-0/resources/conf/paths.txt (Permission denied) from them stdout .. as a quick fix (or the exception could be catched in PS). Then the stdio regex would not complain.

[bernt-matthias]

I might add it, but that would require to add mzml files to the repo as input to MM and they are usually too big to be included there...

We might borrow one from here: #587

Is MM not working with mgf files? Then mgf input to peak_lists_files might lead to problems, or?

[CarlosHorro]

I might add it, but that would require to add mzml files to the repo as input to MM and they are usually too big to be included there...

We might borrow one from here: #587

Is MM not working with mgf files? Then mgf input to peak_lists_files might lead to problems, or?

MetaMorpheus only admits mzml files, yes. I thought about adding a warning text message in the peak_lists_files area, and I am not sure if a validation may be added...

[bernt-matthias]

Just one last question: is it correct that exec_dir is not used anymore for PS?

[bernt-matthias]

Can you respond to #553?

[CarlosHorro]

Can you respond to #553?

Thank you for the reminder, I did not see her question on time.

[CarlosHorro]

Just one last question: is it correct that exec_dir is not used anymore for PS?

Um... that is a good question, I think that using the temporary folder works fine, but now I am not sure about , ie, this searchgui.py code in bioconda :

def jvm_opts(argv):
...
elif arg.startswith('--exec_dir='):
            exec_dir = arg.split('=')[1].strip('"').strip("'")
            if not os.path.exists(exec_dir):
                shutil.copytree(real_dirname(sys.argv[0]), exec_dir, symlinks=False, ignore=None)
                src = real_dirname(sys.argv[0])
                os.remove(os.path.join(exec_dir, "resources/XTandem/linux/linux_64bit/tandem"))
                os.symlink(os.path.join(src, "resources/XTandem/linux/linux_64bit/tandem"),
                           os.path.join(exec_dir, "resources/XTandem/linux/linux_64bit/tandem"))

The piece of code related to xtandem is not being executed anymore, but it seems to work fine (I guess the path existed)...

[CarlosHorro]

About the validator, do you think it is possible to do it @bernt-matthias ? I have done some research and I do not find anything related to a validator that checks the value of 2 different parameters (in this case, the search engines chosen and the file formats introduced) ?

[bernt-matthias]

Um... that is a good question,

Wondering if this could "solve" the paths.txt exception problem since the copy should be writable.

But I would prefer if it works without exec_dir ..

[CarlosHorro]

Um... that is a good question,

Wondering if this could "solve" the paths.txt exception problem since the copy should be writable.

But I would prefer if it works without exec_dir ..

You were right, with the "exec_dir" the paths.txt issue does not show up. What do I do? I am afraid that my time for keeping the tools will not be enough for solving that paths.txt related issue without the exec_dir soon at all...

[bernt-matthias]

What do I do?

I would suggest to try to go the grep way. Can you add a TODO note that exec_dir might not be needed anymore. Then we may remove it from the conda wrapper in the future once this has been tested for a while in the wild.

[bernt-matthias]

Really looking forward that my colleagues can test metamorpheus from SG (they are currently also trying #587).

[CarlosHorro]

I will try to add the MetaMorpheus test today... do I add any comment about the source of the mzML & fasta files for the test, @bernt-matthias ?

[bernt-matthias]

do I add any comment about the source of the mzML & fasta files for the test,

yes. why not

[CarlosHorro]

I think this should make it...

[bernt-matthias]

Thanks @CarlosHorro